The first step is to tap on Cydia and install iFile, a jailbreak application that allows you to access and make changes to the iOS filesystem. You’ll then want to visit this article from an iOS device, tap on one of the Cydia logos in the gallery below and save it to Camera Roll. Further icons are available on deviantART and Reddit.
After that you’ve chosen the logo, follow the following steps:
STEP 1: Navigate to /var/mobile/Media/DCIM/100APPLE to find the logo you just saved. It should be near the bottom of the list.
STEP 2: Tap on Edit in the top menu, select the logo, tap the clipboard icon in the bottom menu and select Copy/Link.
STEP 3: Navigate to /Applications/Cydia.app.
STEP 4: Tap on Edit in the top menu, followed by the clipboard icon, and select Paste.
STEP 5: Find icon@2x.png in the same folder, tap the blue arrow icon to the right of it and rename the file to something similar. Tap Done when finished.
STEP 6: Rename the logo you pasted to icon@2x.png by tapping the blue arrow icon to the right of it. Tap Done when finished.
STEP 7: Respring or restart your device.
As such, it is highly recommended that you backup your device to iTunes or iCloud beforehand. Let us know how you fare in the comments.